The Purkinje cell degeneration (pcd) mouse is a recessive model of neurodegeneration, involving the retina and cerebellum, with a phenotype of ataxia and blindness. Purkinje cell death in pcd is dramatic, as > 99% of post-developmental Purkinje neurons are lost in three weeks. Loss-of-function of Nna1 causes pcd, and Nna1 is a highly conserved protease (zinc carboxypeptidase). In this project, we pursued a broad range of experiments to determine why Nna1 loss-of-function results in retinal and cerebellar degeneration in pcd mice. Each approach has yielded significant insights into Nna1 function, the cell death process in Purkinje cell neurons, and the biology of retinal photoreceptors. We discovered the molecular basis of the pcd-5J mutation, and proved that the carboxypeptidase activity of Nna1 is required to prevent both retinal photoreceptor loss and Purkinje cell degeneration in pcd. We found that autophagy activation and enhanced mitophagy are involved in pcd Purkinje cell death. We obtained loss-of-function alleles of the Drosophila Nna1 orthologue (NnaD) and discovered that reduced NnaD function yields a semi-lethal phenotype, with survivors displaying phenotypes that mirror the pathology observed in pcd mice. Finally, we linked Nna1-NnaD proteins with mitochondrial metabolic functions by quantitative proteomics studies of pcd mice and ultrastructural analysis of NnaD loss-of-function flies and pcd mice. Our discovery of a role for Nna1 loss-of-function in mitochondrial dysfunction and our documentation of increased mitophagy in degenerating neurons provide us with a unique opportunity to delineate mechanistic relationships between altered mitochondrial function and mitophagy. Furthermore, our recent observation that diminished Drp1-dependent mitochondrial fission can rescue degenerative phenotypes in NnaD flies suggests a connection between mitochondrial metabolic function, mitochondrial turnover, mitochondrial dynamics and neuron cell death. In this renewal, we will advance our knowledge of Nna1 protein function, pcd neuron degeneration, and neuronal mitochondrial biology. First, we will determine if Nna1-NnaD localizes to the mitochondria. Second, we will continue our studies of the Nna1 interactome by confirming proteomically predicted protein interactions and characterizing confirmed interactions, assaying interacting proteins as substrates for Nna1 carboxypeptidase activity, and testing if interacting proteins are involved in NnaD - Nna1 loss-of-function pathways. Third, we will evaluate the role of altered autophagy in pcd neurodegeneration, and fourth, we will determine if Nna1 plays a role in mitochondrial dynamics and if altered mitochondrial dynamics is contributing to neuron cell death in pcd mice. Thus, we will establish the intersection between Nna loss-of-function and mitochondrial pathways, in the hope that this will allow us to delineate how mitochondrial dysfunction occurs in a range of neurological diseases.